diff --git a/tests/pipeline/test.nf.test b/tests/pipeline/test.nf.test index a1593bf7..e916bcc6 100644 --- a/tests/pipeline/test.nf.test +++ b/tests/pipeline/test.nf.test @@ -31,8 +31,8 @@ nextflow_pipeline { path("$outputDir/db_tables/proteins_peptides.tsv"), path("$outputDir/db_tables/peptides.tsv.gz"), path("$outputDir/db_tables/proteins.tsv.gz"), + path("$outputDir/db_tables/predictions.tsv.gz"), path("$outputDir/db_tables/stats.txt")).match("db_tables") }, - { assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() }, diff --git a/tests/pipeline/test.nf.test.snap b/tests/pipeline/test.nf.test.snap index a2453f14..4a3003b5 100644 --- a/tests/pipeline/test.nf.test.snap +++ b/tests/pipeline/test.nf.test.snap @@ -4,21 +4,33 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,e865774e32935a69306461ff47428aa8", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,d008f6c7518e9932de2159751cb2519c", + "entities_proteins.tsv:md5,58bec9a717a9ea802cedf258db60efaa", "entities.tsv:md5,5aa057079ae45d1e0fd86ebcaa18af0f", "microbiomes_entities.no_weights.tsv:md5,4d45837586c7c6dc4a19b41735215b01", "microbiomes_entities.nucl.tsv:md5,f5a3ff3cc1f8100f56238b9fab405e66", "microbiomes_entities.tsv:md5,37690c15b6151ff0622130b8672cddb1", "microbiomes.tsv:md5,20f141ba0c97325e9d99a9c0765f9a37", - "proteins_peptides.tsv:md5,09f90e7895eca070c9301a4b818fa240", - "stats.txt:md5,83204291158696ce5d19c4e976f38efe" + "proteins_peptides.tsv:md5,58547bc2efb9ae4f154710bb58d14c54", + "peptides.tsv.gz:md5,66f6ceef1d5212d061b46c90703282d9", + "proteins.tsv.gz:md5,07964ef2abee962131338b180399a4ee", + "predictions.tsv.gz:md5,c833bdb8d00e719b83e5decd1644c2c9", + "stats.txt:md5,910aff94c66e62a31d28dda6e03b916f" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T18:08:31.711958907" }, "logs": { "content": [ - "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-06-26T08:14:54+0000" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_all.nf.test b/tests/pipeline/test_all.nf.test index c579d301..d1cb45e5 100644 --- a/tests/pipeline/test_all.nf.test +++ b/tests/pipeline/test_all.nf.test @@ -22,19 +22,18 @@ nextflow_pipeline { { assert snapshot(path("$outputDir/db_tables/alleles.tsv"), path("$outputDir/db_tables/conditions_alleles.tsv"), path("$outputDir/db_tables/conditions.tsv"), + path("$outputDir/db_tables/entities_proteins.tsv"), path("$outputDir/db_tables/entities.tsv"), + path("$outputDir/db_tables/microbiomes_entities.no_weights.tsv"), path("$outputDir/db_tables/microbiomes_entities.nucl.tsv"), + path("$outputDir/db_tables/microbiomes_entities.tsv"), path("$outputDir/db_tables/microbiomes.tsv"), + path("$outputDir/db_tables/proteins_peptides.tsv"), path("$outputDir/db_tables/peptides.tsv.gz"), path("$outputDir/db_tables/proteins.tsv.gz"), - path("$outputDir/db_tables/entities_proteins.tsv"), - path("$outputDir/db_tables/microbiomes_entities.no_weights.tsv"), - path("$outputDir/db_tables/microbiomes_entities.tsv"), - path("$outputDir/db_tables/proteins_peptides.tsv"), + path("$outputDir/db_tables/predictions.tsv.gz"), path("$outputDir/db_tables/stats.txt")).match("db_tables") }, - { assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() }, - { assert snapshot(path("$outputDir/entrez_data/microbiomes_entities.entrez.tsv")).match("entrez_data") }, { assert new File("$outputDir/entrez_data/entities_proteins.entrez.tsv").exists() }, { assert new File("$outputDir/entrez_data/proteins.entrez.tsv.gz").exists() }, diff --git a/tests/pipeline/test_all.nf.test.snap b/tests/pipeline/test_all.nf.test.snap index 4b9f879c..dcd1d1ab 100644 --- a/tests/pipeline/test_all.nf.test.snap +++ b/tests/pipeline/test_all.nf.test.snap @@ -1,26 +1,46 @@ { + "entrez_data": { + "content": [ + "microbiomes_entities.entrez.tsv:md5,77463a684452d34795b6eda52cfad072" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-26T08:14:54+0000" + }, "db_tables": { "content": [ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,0e992c19471bb56c9b6e6a6f71302742", "conditions.tsv:md5,87707cd0dee14b0ca4face090ba9dce9", + "entities_proteins.tsv:md5,dfb070f991b705ad1d85dd48dcd5dd0c", "entities.tsv:md5,8ae4f7ebc592712f45dea1ceaf5a18c0", + "microbiomes_entities.no_weights.tsv:md5,19a44189e6977fc64b78198ad609507a", "microbiomes_entities.nucl.tsv:md5,aa0d4cc3546508c8e5b81bc9b4b16e39", + "microbiomes_entities.tsv:md5,78b8a81a3abca87ddca748efd14c64ec", "microbiomes.tsv:md5,70871c8b3023f5a8412c05f4a69dda2f", - "stats.txt:md5,896155e0f043f30bd71c38c8ee7b466c" - ], - "timestamp": "2024-06-26T08:14:54+0000" - }, - "entrez_data": { - "content": [ - "microbiomes_entities.entrez.tsv:md5,77463a684452d34795b6eda52cfad072" + "proteins_peptides.tsv:md5,1c0a8c8ea8fbd85d0576714b5220b411", + "peptides.tsv.gz:md5,36aba6d50b1aad95859a547b06d04fc5", + "proteins.tsv.gz:md5,b8c74032604f6ef5c3d73fdf8950aa6b", + "predictions.tsv.gz:md5,96d585b8d153fa93681c80f1bf02290f", + "stats.txt:md5,b04463d0268b44814c2a1170a28b1a86" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T19:59:33.708954186" }, "logs": { "content": [ - "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T11:53:04.064515848" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_assembly_only.nf.test b/tests/pipeline/test_assembly_only.nf.test index beefd0ba..9f95156e 100644 --- a/tests/pipeline/test_assembly_only.nf.test +++ b/tests/pipeline/test_assembly_only.nf.test @@ -32,8 +32,8 @@ nextflow_pipeline { path("$outputDir/db_tables/proteins_peptides.tsv"), path("$outputDir/db_tables/peptides.tsv.gz"), path("$outputDir/db_tables/proteins.tsv.gz"), + path("$outputDir/db_tables/predictions.tsv.gz"), path("$outputDir/db_tables/stats.txt")).match("db_tables") }, - { assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() }, diff --git a/tests/pipeline/test_assembly_only.nf.test.snap b/tests/pipeline/test_assembly_only.nf.test.snap index 9c1405d9..7401711f 100644 --- a/tests/pipeline/test_assembly_only.nf.test.snap +++ b/tests/pipeline/test_assembly_only.nf.test.snap @@ -4,21 +4,33 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,3f2946abda456ffd970aca5a7a4eddf6", + "entities_proteins.tsv:md5,68b046dde6642a0254515588bf3b0ae6", "entities.tsv:md5,52312b19a8f3e5c4412afa130179c145", "microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19", "microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7", "microbiomes_entities.tsv:md5,ed8996c0b489a36f0d88caf68eafe68e", "microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128", - "proteins_peptides.tsv:md5,fea5ec6926a79d562fe7995db16b4af0", + "proteins_peptides.tsv:md5,ff31eacf91875205291a83f742350318", + "peptides.tsv.gz:md5,dd0f94bea5079df8ef06895de255038b", + "proteins.tsv.gz:md5,104b786dfa89e183a46e29f1f37f17de", + "predictions.tsv.gz:md5,e34159d38c4fb47abb02e2ad250ff138", "stats.txt:md5,d138e30d814db5203a789b7eddd04732" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T18:11:18.888885337" }, "logs": { "content": [ - "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-06-26T08:14:54+0000" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_bins_only.nf.test b/tests/pipeline/test_bins_only.nf.test index 4bc30a19..77c175fb 100644 --- a/tests/pipeline/test_bins_only.nf.test +++ b/tests/pipeline/test_bins_only.nf.test @@ -32,8 +32,8 @@ nextflow_pipeline { path("$outputDir/db_tables/proteins_peptides.tsv"), path("$outputDir/db_tables/peptides.tsv.gz"), path("$outputDir/db_tables/proteins.tsv.gz"), + path("$outputDir/db_tables/predictions.tsv.gz"), path("$outputDir/db_tables/stats.txt")).match("db_tables") }, - { assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() }, diff --git a/tests/pipeline/test_bins_only.nf.test.snap b/tests/pipeline/test_bins_only.nf.test.snap index c72291e9..79c204ad 100644 --- a/tests/pipeline/test_bins_only.nf.test.snap +++ b/tests/pipeline/test_bins_only.nf.test.snap @@ -4,21 +4,33 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f", "conditions.tsv:md5,5b04349198a406fc16760c7e8808bb23", - "entities_proteins.tsv:md5,20e495ff06ccacb0f81dbd65e556fc83", + "entities_proteins.tsv:md5,9701a83abaf10c00ff5d7dc002b01a1c", "entities.tsv:md5,7a472316b8e96e9b12d7ca3ff6a88d39", "microbiomes_entities.no_weights.tsv:md5,bf3ff9d0390b49c6ecafd89c93909b67", "microbiomes_entities.nucl.tsv:md5,84b6b907695caaddc959682504749832", "microbiomes_entities.tsv:md5,2f40573eb52f3d823aad2f09a639eee2", "microbiomes.tsv:md5,3f58c3029d21a59316861c28af4361d1", - "proteins_peptides.tsv:md5,4a41affbbc888802cf9202ec1c2ab8a4", - "stats.txt:md5,62d598a845aff61f2be843daa250f485" + "proteins_peptides.tsv:md5,d93e37f0160156298abbb5106ac10aa5", + "peptides.tsv.gz:md5,34497a1a57af3c3e48fceb762cf94f75", + "proteins.tsv.gz:md5,e3c66cf6c5a54a52478a104f23d0d606", + "predictions.tsv.gz:md5,4699fcd56d1af1dd7f9ed7dd41b7ae64", + "stats.txt:md5,a5ef37919a11263ff387e859d1e8c33c" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T18:48:27.027414679" }, "logs": { "content": [ - "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-06-26T08:14:54+0000" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_coassembly.nf.test b/tests/pipeline/test_coassembly.nf.test index b1152561..bc315296 100644 --- a/tests/pipeline/test_coassembly.nf.test +++ b/tests/pipeline/test_coassembly.nf.test @@ -32,8 +32,8 @@ nextflow_pipeline { path("$outputDir/db_tables/proteins_peptides.tsv"), path("$outputDir/db_tables/peptides.tsv.gz"), path("$outputDir/db_tables/proteins.tsv.gz"), + path("$outputDir/db_tables/predictions.tsv.gz"), path("$outputDir/db_tables/stats.txt")).match("db_tables") }, - { assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() }, diff --git a/tests/pipeline/test_coassembly.nf.test.snap b/tests/pipeline/test_coassembly.nf.test.snap index 9ca01e59..2864ddee 100644 --- a/tests/pipeline/test_coassembly.nf.test.snap +++ b/tests/pipeline/test_coassembly.nf.test.snap @@ -4,21 +4,33 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,ad6438cc0e62033f39629d7d002169b5", "conditions.tsv:md5,092aba068d94feb11b61a22d694359d7", - "entities_proteins.tsv:md5,59e2e25ec73cbdf908d474d4abba6716", + "entities_proteins.tsv:md5,1e64633559bc88f0ce96550d821a2f73", "entities.tsv:md5,e11b4c3cae16172e0643416fe1e55e0e", "microbiomes_entities.no_weights.tsv:md5,45512c04e01b2f652b60c5438377411e", "microbiomes_entities.nucl.tsv:md5,2f884256b54995a265af83b2eb68e773", "microbiomes_entities.tsv:md5,212fd9b2d8fd3340beac070b812f88e9", "microbiomes.tsv:md5,b89503022fcbd9b7d7f9eefe7cbccf0f", - "proteins_peptides.tsv:md5,39bc2a204d8bfb5f01c99451ede47c34", - "stats.txt:md5,f2957aced6994532212f0d25b3efba98" + "proteins_peptides.tsv:md5,58547bc2efb9ae4f154710bb58d14c54", + "peptides.tsv.gz:md5,66f6ceef1d5212d061b46c90703282d9", + "proteins.tsv.gz:md5,2d25ff5eb066f3ddc8aa71a7acf5f3ce", + "predictions.tsv.gz:md5,998fcc2d79f0c9e340dd678187d12635", + "stats.txt:md5,027c733d48c47409486c8c1b4425bb7a" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T19:22:30.912008946" }, "logs": { "content": [ - "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-06-26T08:14:54+0000" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_mhcflurry.nf.test b/tests/pipeline/test_mhcflurry.nf.test index 7acdd085..5fa963a6 100644 --- a/tests/pipeline/test_mhcflurry.nf.test +++ b/tests/pipeline/test_mhcflurry.nf.test @@ -32,8 +32,8 @@ nextflow_pipeline { path("$outputDir/db_tables/proteins_peptides.tsv"), path("$outputDir/db_tables/peptides.tsv.gz"), path("$outputDir/db_tables/proteins.tsv.gz"), + path("$outputDir/db_tables/predictions.tsv.gz"), path("$outputDir/db_tables/stats.txt")).match("db_tables") }, - { assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() }, diff --git a/tests/pipeline/test_mhcflurry.nf.test.snap b/tests/pipeline/test_mhcflurry.nf.test.snap index 60d2fb89..a074b6e9 100644 --- a/tests/pipeline/test_mhcflurry.nf.test.snap +++ b/tests/pipeline/test_mhcflurry.nf.test.snap @@ -4,21 +4,32 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,3f2946abda456ffd970aca5a7a4eddf6", + "entities_proteins.tsv:md5,68b046dde6642a0254515588bf3b0ae6", "entities.tsv:md5,52312b19a8f3e5c4412afa130179c145", "microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19", "microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7", "microbiomes_entities.tsv:md5,ed8996c0b489a36f0d88caf68eafe68e", "microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128", - "proteins_peptides.tsv:md5,fea5ec6926a79d562fe7995db16b4af0", + "proteins_peptides.tsv:md5,ff31eacf91875205291a83f742350318", + "peptides.tsv.gz:md5,dd0f94bea5079df8ef06895de255038b", + "proteins.tsv.gz:md5,104b786dfa89e183a46e29f1f37f17de", + "predictions.tsv.gz:md5,0df02a33f17a057f5da6775a21f73056", "stats.txt:md5,d138e30d814db5203a789b7eddd04732" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-11T08:25:27.152248406" }, "logs": { "content": [ "prediction_warnings.log:md5,d2bb11e8da2c2003b18054bb1e6843ca" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-06-26T08:14:54+0000" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_mhcnuggets_1.nf.test b/tests/pipeline/test_mhcnuggets_1.nf.test index 3a4b25d4..0ae94cb4 100644 --- a/tests/pipeline/test_mhcnuggets_1.nf.test +++ b/tests/pipeline/test_mhcnuggets_1.nf.test @@ -32,8 +32,8 @@ nextflow_pipeline { path("$outputDir/db_tables/proteins_peptides.tsv"), path("$outputDir/db_tables/peptides.tsv.gz"), path("$outputDir/db_tables/proteins.tsv.gz"), + path("$outputDir/db_tables/predictions.tsv.gz"), path("$outputDir/db_tables/stats.txt")).match("db_tables") }, - { assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() }, diff --git a/tests/pipeline/test_mhcnuggets_1.nf.test.snap b/tests/pipeline/test_mhcnuggets_1.nf.test.snap index d2c26b2f..c39ca8b3 100644 --- a/tests/pipeline/test_mhcnuggets_1.nf.test.snap +++ b/tests/pipeline/test_mhcnuggets_1.nf.test.snap @@ -4,21 +4,32 @@ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,3f2946abda456ffd970aca5a7a4eddf6", + "entities_proteins.tsv:md5,68b046dde6642a0254515588bf3b0ae6", "entities.tsv:md5,52312b19a8f3e5c4412afa130179c145", "microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19", "microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7", "microbiomes_entities.tsv:md5,ed8996c0b489a36f0d88caf68eafe68e", "microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128", - "proteins_peptides.tsv:md5,fea5ec6926a79d562fe7995db16b4af0", + "proteins_peptides.tsv:md5,ff31eacf91875205291a83f742350318", + "peptides.tsv.gz:md5,dd0f94bea5079df8ef06895de255038b", + "proteins.tsv.gz:md5,104b786dfa89e183a46e29f1f37f17de", + "predictions.tsv.gz:md5,d6672533fdd7ed61cac6e420a0fccb90", "stats.txt:md5,d138e30d814db5203a789b7eddd04732" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-11T08:27:02.891779522" }, "logs": { "content": [ "prediction_warnings.log:md5,7c11afacf5a3060459cf58d3bd032230" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-06-26T08:14:54+0000" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_mhcnuggets_2.nf.test b/tests/pipeline/test_mhcnuggets_2.nf.test index 54844431..7f87770e 100644 --- a/tests/pipeline/test_mhcnuggets_2.nf.test +++ b/tests/pipeline/test_mhcnuggets_2.nf.test @@ -32,8 +32,8 @@ nextflow_pipeline { path("$outputDir/db_tables/proteins_peptides.tsv"), path("$outputDir/db_tables/peptides.tsv.gz"), path("$outputDir/db_tables/proteins.tsv.gz"), + path("$outputDir/db_tables/predictions.tsv.gz"), path("$outputDir/db_tables/stats.txt")).match("db_tables") }, - { assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.DPB1_01_01.pdf").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.with_points.DPB1_01_01.pdf").exists() }, diff --git a/tests/pipeline/test_mhcnuggets_2.nf.test.snap b/tests/pipeline/test_mhcnuggets_2.nf.test.snap index e099861e..db39d5e2 100644 --- a/tests/pipeline/test_mhcnuggets_2.nf.test.snap +++ b/tests/pipeline/test_mhcnuggets_2.nf.test.snap @@ -4,21 +4,32 @@ "alleles.tsv:md5,ab0e4dbbb55b8154d37256018c19d67c", "conditions_alleles.tsv:md5,769c299e94c7df654a5a14da2771c95d", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,3f2946abda456ffd970aca5a7a4eddf6", + "entities_proteins.tsv:md5,68b046dde6642a0254515588bf3b0ae6", "entities.tsv:md5,52312b19a8f3e5c4412afa130179c145", "microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19", "microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7", "microbiomes_entities.tsv:md5,ed8996c0b489a36f0d88caf68eafe68e", "microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128", - "proteins_peptides.tsv:md5,fea5ec6926a79d562fe7995db16b4af0", + "proteins_peptides.tsv:md5,ff31eacf91875205291a83f742350318", + "peptides.tsv.gz:md5,dd0f94bea5079df8ef06895de255038b", + "proteins.tsv.gz:md5,104b786dfa89e183a46e29f1f37f17de", + "predictions.tsv.gz:md5,aad52bad1c4bf18148bbe64f423ebc0f", "stats.txt:md5,d138e30d814db5203a789b7eddd04732" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-11T08:28:40.388743427" }, "logs": { "content": [ "prediction_warnings.log:md5,d3ff6ac2a68d620e8f5023f4ab16a1b9" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-06-26T08:14:54+0000" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_model_information.nf.test.snap b/tests/pipeline/test_model_information.nf.test.snap index 03b88c1f..29b7a76d 100644 --- a/tests/pipeline/test_model_information.nf.test.snap +++ b/tests/pipeline/test_model_information.nf.test.snap @@ -10,6 +10,10 @@ "syfpeithi.v1.0.supported_alleles.txt:md5,e007149d8f41dafc1290791c5f726194", "syfpeithi.v1.0.supported_lengths.txt:md5,09d2bfbc74ac9aa5bb1a650f02b848df" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T15:13:19.924993689" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_mouse.nf.test b/tests/pipeline/test_mouse.nf.test index aa4a52d7..92718a27 100644 --- a/tests/pipeline/test_mouse.nf.test +++ b/tests/pipeline/test_mouse.nf.test @@ -32,8 +32,8 @@ nextflow_pipeline { path("$outputDir/db_tables/proteins_peptides.tsv"), path("$outputDir/db_tables/peptides.tsv.gz"), path("$outputDir/db_tables/proteins.tsv.gz"), + path("$outputDir/db_tables/predictions.tsv.gz"), path("$outputDir/db_tables/stats.txt")).match("db_tables") }, - { assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() }, { assert snapshot(path("$outputDir/entrez_data/microbiomes_entities.entrez.tsv")).match("entrez_data") }, { assert new File("$outputDir/entrez_data/entities_proteins.entrez.tsv").exists() }, diff --git a/tests/pipeline/test_mouse.nf.test.snap b/tests/pipeline/test_mouse.nf.test.snap index 1a50c325..ab76f3b2 100644 --- a/tests/pipeline/test_mouse.nf.test.snap +++ b/tests/pipeline/test_mouse.nf.test.snap @@ -1,26 +1,46 @@ { + "entrez_data": { + "content": [ + "microbiomes_entities.entrez.tsv:md5,77463a684452d34795b6eda52cfad072" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-26T08:14:54+0000" + }, "db_tables": { "content": [ "alleles.tsv:md5,314847ac5a69fe93ce75c6db0c2496d8", "conditions_alleles.tsv:md5,e865774e32935a69306461ff47428aa8", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", + "entities_proteins.tsv:md5,4d1e6bd45c920b04f74c0f0c1d53efc8", "entities.tsv:md5,1b26a72cb5f731ba04ed53b6e69237b7", + "microbiomes_entities.no_weights.tsv:md5,dc9ec36f31bc43f5aeaeb542a2af3e6b", "microbiomes_entities.nucl.tsv:md5,f5a3ff3cc1f8100f56238b9fab405e66", + "microbiomes_entities.tsv:md5,86346e23fe421e1d9e72bfc955e10db3", "microbiomes.tsv:md5,2130005595bdc7ffc770d8304fd9a936", - "stats.txt:md5,6e5ecca241fb1cd3fea7ea66c4b81e2a" - ], - "timestamp": "2024-06-26T08:14:54+0000" - }, - "entrez_data": { - "content": [ - "microbiomes_entities.entrez.tsv:md5,77463a684452d34795b6eda52cfad072" + "proteins_peptides.tsv:md5,a17cd18e1fe9ad73d8e18d241f77c0c2", + "peptides.tsv.gz:md5,260d711f2ea11fb3327f3eff6b6a7516", + "proteins.tsv.gz:md5,328b977d64261bb5c45b34ce10d261a7", + "predictions.tsv.gz:md5,e15f5ca311bb8ede869104eb267d00fa", + "stats.txt:md5,8ba4d24d65db50958f31f97fecbbe24e" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T20:02:29.928405814" }, "logs": { "content": [ - "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "WARNING_unify_peptide_lengths.log:md5,c554eace446f21ad0c7990c92554edb0" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T11:56:01.153832945" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_mouse_all_pep_lengths.nf.test b/tests/pipeline/test_mouse_all_pep_lengths.nf.test index 447e7a9f..c5588c01 100644 --- a/tests/pipeline/test_mouse_all_pep_lengths.nf.test +++ b/tests/pipeline/test_mouse_all_pep_lengths.nf.test @@ -32,8 +32,8 @@ nextflow_pipeline { path("$outputDir/db_tables/proteins_peptides.tsv"), path("$outputDir/db_tables/peptides.tsv.gz"), path("$outputDir/db_tables/proteins.tsv.gz"), + path("$outputDir/db_tables/predictions.tsv.gz"), path("$outputDir/db_tables/stats.txt")).match("db_tables") }, - { assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.H2-Db.pdf").exists() }, { assert new File("$outputDir/figures/entity_binding_ratios.with_points.H2-Db.pdf").exists() }, diff --git a/tests/pipeline/test_mouse_all_pep_lengths.nf.test.snap b/tests/pipeline/test_mouse_all_pep_lengths.nf.test.snap index c30ae4e5..f988e882 100644 --- a/tests/pipeline/test_mouse_all_pep_lengths.nf.test.snap +++ b/tests/pipeline/test_mouse_all_pep_lengths.nf.test.snap @@ -4,21 +4,32 @@ "alleles.tsv:md5,314847ac5a69fe93ce75c6db0c2496d8", "conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,3f2946abda456ffd970aca5a7a4eddf6", + "entities_proteins.tsv:md5,68b046dde6642a0254515588bf3b0ae6", "entities.tsv:md5,52312b19a8f3e5c4412afa130179c145", "microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19", "microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7", "microbiomes_entities.tsv:md5,ed8996c0b489a36f0d88caf68eafe68e", "microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128", - "proteins_peptides.tsv:md5,6ae79b31efbc4fd045e68d6f8fedae16", + "proteins_peptides.tsv:md5,8e869d3583e301e1079cdec28f923d2e", + "peptides.tsv.gz:md5,d3120ff2e6c4599883e958605ea7089a", + "proteins.tsv.gz:md5,104b786dfa89e183a46e29f1f37f17de", + "predictions.tsv.gz:md5,73c9928688cd67eecca5d3ef6e833f83", "stats.txt:md5,2675aa8f40b92d9df9c1537d77e8ade1" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T18:09:54.740979846" }, "logs": { "content": [ "prediction_warnings.log:md5,9d5716a14848b2e7ec5766cb1c1c2bf5" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-06-26T08:14:54+0000" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_taxa_only.nf.test b/tests/pipeline/test_taxa_only.nf.test index a7f1fb3a..0af079d4 100644 --- a/tests/pipeline/test_taxa_only.nf.test +++ b/tests/pipeline/test_taxa_only.nf.test @@ -32,8 +32,8 @@ nextflow_pipeline { path("$outputDir/db_tables/proteins_peptides.tsv"), path("$outputDir/db_tables/peptides.tsv.gz"), path("$outputDir/db_tables/proteins.tsv.gz"), + path("$outputDir/db_tables/predictions.tsv.gz"), path("$outputDir/db_tables/stats.txt")).match("db_tables") }, - { assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() }, { assert snapshot(path("$outputDir/entrez_data/microbiomes_entities.entrez.tsv")).match("entrez_data") }, { assert new File("$outputDir/entrez_data/entities_proteins.entrez.tsv").exists() }, diff --git a/tests/pipeline/test_taxa_only.nf.test.snap b/tests/pipeline/test_taxa_only.nf.test.snap index 385379d3..521b5b35 100644 --- a/tests/pipeline/test_taxa_only.nf.test.snap +++ b/tests/pipeline/test_taxa_only.nf.test.snap @@ -1,26 +1,46 @@ { + "entrez_data": { + "content": [ + "microbiomes_entities.entrez.tsv:md5,d74ec125c02485cae58a08a334bf4844" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-26T08:14:54+0000" + }, "db_tables": { "content": [ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", + "entities_proteins.tsv:md5,04ffe2b3aab37d78a4330bbea6f95821", "entities.tsv:md5,c766a12bbb1d4ef4707be7077f774191", + "microbiomes_entities.no_weights.tsv:md5,4ca0afaa5fb1a3f4960c775ad24ae363", "microbiomes_entities.nucl.tsv:md5,84b6b907695caaddc959682504749832", + "microbiomes_entities.tsv:md5,986a063182a36d0515e1d1b31f0e49fa", "microbiomes.tsv:md5,05bafa72c953e6cb0bd72c296d6fe707", + "proteins_peptides.tsv:md5,22f41ed9483a67b2f7644fb5f7b61eda", + "peptides.tsv.gz:md5,0e3c1e87feb2aac34de1ba3b246f27ca", + "proteins.tsv.gz:md5,6f8d47a842ce55855f0075fd48455397", + "predictions.tsv.gz:md5,4f802d81884bcb23545b17a6e8f5cd1d", "stats.txt:md5,c10c27a1ba080ff59dcb5b62467129b2" ], - "timestamp": "2024-06-26T08:14:54+0000" - }, - "entrez_data": { - "content": [ - "microbiomes_entities.entrez.tsv:md5,d74ec125c02485cae58a08a334bf4844" - ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T20:08:12.631077076" }, "logs": { "content": [ - "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T11:07:57.477692224" } -} +} \ No newline at end of file diff --git a/tests/pipeline/test_taxa_specific_assembly.nf.test b/tests/pipeline/test_taxa_specific_assembly.nf.test index 8a1489ab..2f567c49 100644 --- a/tests/pipeline/test_taxa_specific_assembly.nf.test +++ b/tests/pipeline/test_taxa_specific_assembly.nf.test @@ -32,8 +32,8 @@ nextflow_pipeline { path("$outputDir/db_tables/proteins_peptides.tsv"), path("$outputDir/db_tables/peptides.tsv.gz"), path("$outputDir/db_tables/proteins.tsv.gz"), + path("$outputDir/db_tables/predictions.tsv.gz"), path("$outputDir/db_tables/stats.txt")).match("db_tables") }, - { assert new File("$outputDir/db_tables/predictions.tsv.gz").exists() }, { assert snapshot(path("$outputDir/entrez_data/microbiomes_entities.entrez.tsv")).match("entrez_data") }, { assert new File("$outputDir/entrez_data/entities_proteins.entrez.tsv").exists() }, diff --git a/tests/pipeline/test_taxa_specific_assembly.nf.test.snap b/tests/pipeline/test_taxa_specific_assembly.nf.test.snap index 06a3fc36..53a6a15c 100644 --- a/tests/pipeline/test_taxa_specific_assembly.nf.test.snap +++ b/tests/pipeline/test_taxa_specific_assembly.nf.test.snap @@ -1,30 +1,46 @@ { + "entrez_data": { + "content": [ + "microbiomes_entities.entrez.tsv:md5,d74ec125c02485cae58a08a334bf4844" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-26T08:14:54+0000" + }, "db_tables": { "content": [ "alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa", "conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f", "conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c", - "entities_proteins.tsv:md5,7974796e978a93986c52f571ad8c6ae4", + "entities_proteins.tsv:md5,04ffe2b3aab37d78a4330bbea6f95821", "entities.tsv:md5,c766a12bbb1d4ef4707be7077f774191", "microbiomes_entities.no_weights.tsv:md5,4ca0afaa5fb1a3f4960c775ad24ae363", "microbiomes_entities.nucl.tsv:md5,84b6b907695caaddc959682504749832", "microbiomes_entities.tsv:md5,986a063182a36d0515e1d1b31f0e49fa", "microbiomes.tsv:md5,02bf660f1c06ace8993249ef6b527385", - "proteins_peptides.tsv:md5,c203974186782d898355654ce5b35803", + "proteins_peptides.tsv:md5,22f41ed9483a67b2f7644fb5f7b61eda", + "peptides.tsv.gz:md5,0e3c1e87feb2aac34de1ba3b246f27ca", + "proteins.tsv.gz:md5,6f8d47a842ce55855f0075fd48455397", + "predictions.tsv.gz:md5,4f802d81884bcb23545b17a6e8f5cd1d", "stats.txt:md5,c10c27a1ba080ff59dcb5b62467129b2" ], - "timestamp": "2024-06-26T08:14:54+0000" - }, - "entrez_data": { - "content": [ - "microbiomes_entities.entrez.tsv:md5,d74ec125c02485cae58a08a334bf4844" - ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T20:13:49.986930974" }, "logs": { "content": [ - "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55" ], - "timestamp": "2024-06-26T08:14:54+0000" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-10T12:07:04.049737935" } -} +} \ No newline at end of file diff --git a/workflows/metapep.nf b/workflows/metapep.nf index 794bfab6..7496f9e3 100644 --- a/workflows/metapep.nf +++ b/workflows/metapep.nf @@ -216,8 +216,8 @@ workflow METAPEP { ch_merge_predictions_input_warn = MERGE_PREDICTIONS_BUFFER.out.ch_prediction_warnings_merged_buffer.mix(ch_predictions_unbuffered.warnings) MERGE_PREDICTIONS ( - ch_merge_predictions_input_pred.collect(), - ch_merge_predictions_input_warn.collect() + ch_merge_predictions_input_pred.collect(sort: { it.baseName }), + ch_merge_predictions_input_warn.collect(sort: { it.baseName }) ) ch_versions = ch_versions.mix(MERGE_PREDICTIONS.out.versions)